Gravity Assist (GA) is a kind of transfer orbit technology widely used in interplanetary missions, which highly depends on navigation performance to succeed. The Orbital Dynamic Equation is an essential component in the navigation system, affected by factors including the numerical integrator, perturbing planets, integration step size, gravitational constant and planet ephemerides. To analyse the impact factors mentioned above and investigate an efficient system model, the propagation and navigation results are carried out in a Mars-assist explorer scenario; a specific case study is also provided in this paper. The results indicate that the planetary ephemeris uncertainty and integration size are the dominant error sources, and the integration step size is the dominant impact factor on the real-time performance. In this specific case, the ‘Orbital Dynamic Equation’ considering Sun and Mars perturbation is suggested for integration by RK4 with 60 s integration step size. The conclusions drawn by this study are particularly useful in the design, construction, and analysis of an autonomous navigation system for a GA explorer.